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Scaffold, Villager, BioCyc, Star-P 2.5 for Python, eMolecules, BioPathwise DM

Geneva Bioinformatics and Proteome Software have integrated GeneBio’s Phenyx software platform for mass spectrometry data analysis into Proteome’s Scaffold proteomics meta-analysis software. The integration gives users increased access to available results, the companies said.
Phenyx identifies and characterizes proteins and peptides from MS data, while
Scaffold statistically validates peptides and proteins from tandem mass spectrometry results. Scaffold considers the results form multiple search engines including Phenyx, Sequest, or Mascot, as well as optionally running X!Tandem on data files for cross-validation.

Transgenic Software has announced a Microsoft SQL Server 2005 version of its Villager Transgenic Animal Management System, a laboratory information-management system that develops, breeds, and tracks transgenic and knockout animal models.
The server version furthers the company’s transgenic workflow control technology and bolsters integration with the Microsoft Office development platform, the company said.

SRI International has released version 11.1 of the BioCyc suite of databases. EcoCyc 11.1 includes six new metabolic pathways, while MetaCyc 11.1 has been enhanced to offer 39 new pathways and 31 revised pathways that include new commentary and updated enzyme and gene identification. MetaCyc also includes a new “superpathway,” for a combined 71 new and updated pathways. 
The new version also expands coverage of fermentation pathways; the metabolism of glutamate, glutamine, aspartate, and asparagine; and the degradation of parathion and related compounds.

Interactive Supercomputing has launched Star-P 2.5 for Python, a new version of its parallel computing software that is compatible with the open source programming language Python.
Star-P for Python enables users to code algorithms on their desktops using Python, but run them on parallel high performance computers, ISC said. It includes a new client interface that lets users take advantage of Python-specific numerical libraries and functions such as NumPy and SciPy.
Python is the second major programming client supported by Star-P, following the platform’s current support for Matlab.
Star-P 2.5 for Python will ship at the end of June and starts at $7,995 for commercial users and $2,495 for academic institutions.
More information is available here.

eMolecules has released version 2.0 of its freely available chemical search engine. Available here, version 2 includes an improved user interface and more than 6 million compounds from 150 suppliers, the company said.   

The BioAnalytics Group has launched BioPathwise DM, a data-management software package for biological data.The server-based system enables groups of researchers to store, and share data along with any reports, records, peer-reviewed journals, or other information.

Filed under

The Scan

mRNA-Based Vaccine on the Way in China

China may soon have its own mRNA-based vaccine, according to Nature News.

Arranged Killing, Fraud Alleged by Prosecutors

The Wall Street Journal reports that prosecutors allege that the co-founder of a biotech arranged to have a business associate who threatened to expose him as a fraud killed.

Whirlwind Decade of CRISPR

The New York Times looks back at the 10 years since the University of California, Berkeley's Jennifer Doudna and her colleagues published their CRISPR paper.

PNAS Papers on Blue Cone Monochromacy Structural Variants, HIV-1 Mutant, T-ALL

In PNAS this week: structural variants linked to blue cone monochromacy, HIV-1 variants affecting the matrix protein p17, and more.